Honestly, with the sheer level of backlash, I wouldn't be surprised if the system was toned down. Not stopped entirely, but scaled back significantly. The fact that Twitch's own shows have been muted says a lot about how badly this was implemented.
Odds are, we're looking at this sort of chronology:
* At some point in the past, Twitch was told it needed to deal with DCMA requests. Most likely, this came from Google, their (soon-to-be?) owners.
* Today, Twitch implements heavy-handed changes to handle DCMA requests, guaranteeing a massive backlash.
* Tomorrow, Twitch openly solicits feedback, in the form of a Reddit AMA (which they advertised in the blog post).
* Tomorrow evening, Twitch goes to their (soon-to-be?) owners, and explains "we received unanimous feedback that this was a terrible idea that will destroy our fanbase. You sure you want us to go ahead with it?"
* The day after tomorrow, Twitch announces that their content censoring algorithm is 'undergoing changes in response to your feedback'.
* Early next week, the system is scaled back. Videos are still muted, but only for short periods of time. Appeals are handled in an automated fashion, allowing attentive streamers to quickly respond when their VODs are muted. The system is still harsher than the previous system (of no checks whatsoever), but Twitch is lauded for softening the blow. (Classic negotiating strategy: demand everything, then only demand half as much. People think you're 'meeting halfway'!)